zkamvar
commented
9 years ago The algorithm for the index of association is detailed in the algorithms and equations vignette.
With SNP data, it is not immediately clear whether or not the markers are linked. It might be a good idea to explore three options for calculating this statistic:
- calculate it over the whole data set (least likely)
- utilize a sliding window on all snps within m nucleotides (could be biased due to SNP proximity)
- randomly sample x SNPs with the constraint that they be m nucleotides apart
- randomly sample x SNPs regardless of position
Neither of these methods are perfect, but it would be useful to see if they are implementable and if they produce meaningful results.
Tasklist:
- [ ] implement basic algorithm for calculating index of association on a genlight object with a small number (< 200) of SNPs.
- [ ] include naive sampling.
- [ ] include sliding window.
- [ ] include sampling to maximize the distance between SNPs.
Implement a sliding window analysis of the index of association and standardized index of association.